2015
An RNA motif advances transcription by preventing Rho-dependent termination
Sevostyanova A, Groisman EA. An RNA motif advances transcription by preventing Rho-dependent termination. Proceedings Of The National Academy Of Sciences Of The United States Of America 2015, 112: e6835-e6843. PMID: 26630006, PMCID: PMC4687561, DOI: 10.1073/pnas.1515383112.Peer-Reviewed Original ResearchConceptsRho-dependent transcription terminationTranscription terminationRNA elementsNucleic Acid Binding ProteinsRho-dependent terminationOpen reading frameRNA polymeraseReading frameBacterial RNALeader regionRNA motifsRNA conformationRho's accessInefficient translationBinding proteinInactive complexPharmacological inhibitionRhoTranscriptionThe Bacterial Transcription Termination Factor Rho Coordinates Mg2+ Homeostasis with Translational Signals
Kriner MA, Groisman EA. The Bacterial Transcription Termination Factor Rho Coordinates Mg2+ Homeostasis with Translational Signals. Journal Of Molecular Biology 2015, 427: 3834-3849. PMID: 26523680, PMCID: PMC4964609, DOI: 10.1016/j.jmb.2015.10.020.Peer-Reviewed Original ResearchMeSH Keywords5' Untranslated RegionsAmino Acid SequenceBacterial ProteinsBase SequenceCation Transport ProteinsGene Expression Regulation, BacterialHomeostasisInverted Repeat SequencesMagnesiumMolecular Sequence DataNucleic Acid ConformationProtein BiosynthesisRho FactorSalmonella typhimuriumTranscription Initiation SiteConceptsLeader regionTranslational signalsGenome-wide activityShort open reading framesRho utilization siteRho-dependent terminationRho-dependent terminatorsOpen reading frameSalmonella enterica serovar TyphimuriumNascent RNATranscription terminationEnterica serovar TyphimuriumTransport genesProtein RhoRNA polymeraseReading frameLeader mRNASpecific genesRNA conformationEfficient translationExclusive conformationsTranscriptionSerovar TyphimuriumGenesRhoFlagella-independent surface motility in Salmonella enterica serovar Typhimurium
Park SY, Pontes MH, Groisman EA. Flagella-independent surface motility in Salmonella enterica serovar Typhimurium. Proceedings Of The National Academy Of Sciences Of The United States Of America 2015, 112: 1850-1855. PMID: 25624475, PMCID: PMC4330729, DOI: 10.1073/pnas.1422938112.Peer-Reviewed Original ResearchMeSH KeywordsAdenosine TriphosphatasesAmino Acid SequenceBacterial ProteinsBase SequenceCation Transport ProteinsComputational BiologyFlagellaGene Expression Regulation, BacterialMagnesiumMembrane Transport ProteinsMitochondrial Proton-Translocating ATPasesMolecular Sequence DataMovementMutagenesisSalmonella typhimuriumSequence AlignmentSequence Analysis, DNAConceptsSalmonella enterica serovar TyphimuriumEnterica serovar TyphimuriumPhoP/PhoQ regulatory systemMgtC mutantFlagellum-independent mannerFlagella-mediated motilitySerovar TyphimuriumForm of motilityWild-type SalmonellaNull mutantsMultiprotein complexesMgtC proteinF1Fo-ATPaseHeterologous promoterSmall proteinsUnknown functionProteinase K treatmentSurface motilityMgtAMutantsGroup motilityAllelic formsRegulatory systemBacterial replicationGenes
2014
Unusually long-lived pause required for regulation of a Rho-dependent transcription terminator
Hollands K, Sevostiyanova A, Groisman EA. Unusually long-lived pause required for regulation of a Rho-dependent transcription terminator. Proceedings Of The National Academy Of Sciences Of The United States Of America 2014, 111: e1999-e2007. PMID: 24778260, PMCID: PMC4024889, DOI: 10.1073/pnas.1319193111.Peer-Reviewed Original ResearchMeSH KeywordsAdenosine TriphosphatasesBacterial ProteinsBase SequenceDNA-Directed RNA PolymerasesGene Expression Regulation, BacterialMagnesiumMembrane Transport ProteinsMolecular Sequence DataNucleic Acid ConformationRho FactorRiboswitchRNA, BacterialRNA, MessengerSalmonella entericaTerminator Regions, GeneticConceptsRho-dependent terminationRho-dependent terminatorsRho-dependent transcription terminatorsTranscription termination eventsTermination eventsTranscription terminationTranscription terminatorPause sitesSuch terminatorsSequence elementsAcid sequenceLeader regionNucleic acid sequencesMolecular determinantsSpecific signalsTerminatorRemarkable longevitySalmonella entericaRhoRegulationSingle siteControl of a Salmonella virulence operon by proline-charged tRNAPro
Lee EJ, Choi J, Groisman EA. Control of a Salmonella virulence operon by proline-charged tRNAPro. Proceedings Of The National Academy Of Sciences Of The United States Of America 2014, 111: 3140-3145. PMID: 24516160, PMCID: PMC3939920, DOI: 10.1073/pnas.1316209111.Peer-Reviewed Original Research5' Untranslated RegionsAmino Acid SequenceAnimalsBacterial ProteinsBase PairingBase SequenceCation Transport ProteinsCodonGene Expression Regulation, BacterialHost-Pathogen InteractionsMiceMolecular Sequence DataOligodeoxyribonucleotidesOpen Reading FramesProlineReal-Time Polymerase Chain ReactionRNA, Transfer, ProSalmonella typhimuriumVirulence
2012
Control of a Salmonella virulence locus by an ATP-sensing leader messenger RNA
Lee EJ, Groisman EA. Control of a Salmonella virulence locus by an ATP-sensing leader messenger RNA. Nature 2012, 486: 271-275. PMID: 22699622, PMCID: PMC3711680, DOI: 10.1038/nature11090.Peer-Reviewed Original ResearchMeSH Keywords5' Untranslated RegionsAdenosine TriphosphateAnimalsBacterial ProteinsBase SequenceCation Transport ProteinsFemaleGene Expression Regulation, BacterialHydrogen-Ion ConcentrationMacrophagesMiceMice, Inbred C3HMolecular Sequence DataMutationSalmonella InfectionsSalmonella typhimuriumSequence AlignmentVirulenceThe promoter architectural landscape of the Salmonella PhoP regulon
Zwir I, Latifi T, Perez JC, Huang H, Groisman EA. The promoter architectural landscape of the Salmonella PhoP regulon. Molecular Microbiology 2012, 84: 463-485. PMID: 22435712, PMCID: PMC3335776, DOI: 10.1111/j.1365-2958.2012.08036.x.Peer-Reviewed Original ResearchConceptsPromoter architectureDistinct promoter architecturesPathogen Salmonella enterica serovar TyphimuriumGene expression behaviorSalmonella enterica serovar TyphimuriumEnterica serovar TyphimuriumPhoP regulonPromoter featuresBiochemical functionsPhoPExpression behaviorPhysiological roleBacterial activatorsGenesSerovar TyphimuriumPromoterRegulonDifferent mechanismsTranscriptionVirulenceActivatorAncestryExpressionLarge numberLimited numberRiboswitch control of Rho-dependent transcription termination
Hollands K, Proshkin S, Sklyarova S, Epshtein V, Mironov A, Nudler E, Groisman EA. Riboswitch control of Rho-dependent transcription termination. Proceedings Of The National Academy Of Sciences Of The United States Of America 2012, 109: 5376-5381. PMID: 22431636, PMCID: PMC3325659, DOI: 10.1073/pnas.1112211109.Peer-Reviewed Original ResearchMeSH KeywordsBase SequenceMolecular Sequence DataNucleic Acid ConformationRho GTP-Binding ProteinsRiboswitchTerminator Regions, GeneticTranscription, GeneticConceptsRho-dependent transcription terminationTranscription terminationRiboswitch ligandsGene expressionControl gene expressionRho-specific inhibitorIntrinsic transcription terminationATPase activityActivity of RhoSalmonella enterica serovar TyphimuriumRiboswitch actionRiboswitch controlTranscription machineryProtein effectorsGene regulationRho ATPase activityEnterica serovar TyphimuriumTranslation initiationThird general mechanismRiboswitchTranscriptionEscherichia coliRNA sensorsWidespread modeSerovar Typhimurium
2011
Ancestral Genes Can Control the Ability of Horizontally Acquired Loci to Confer New Traits
Chen HD, Jewett MW, Groisman EA. Ancestral Genes Can Control the Ability of Horizontally Acquired Loci to Confer New Traits. PLOS Genetics 2011, 7: e1002184. PMID: 21811415, PMCID: PMC3140997, DOI: 10.1371/journal.pgen.1002184.Peer-Reviewed Original ResearchMeSH KeywordsAnti-Bacterial AgentsBacterial ProteinsDNA, BacterialDrug Resistance, BacterialEscherichia coliEscherichia coli ProteinsGene Expression Regulation, BacterialGene Transfer, HorizontalKineticsMagnesiumMolecular Sequence DataPhosphorylationPolymyxin BReverse Transcriptase Polymerase Chain ReactionSalmonella typhimuriumSequence Analysis, DNATranscription FactorsTransformation, BacterialConceptsGene productsPmrD proteinPmrA/PmrB systemSpecies-specific traitsPmrA/PmrBE. coliHigh phosphatase activityBacterium Escherichia coliTwo-component systemPmrA proteinPolymyxin B resistanceAncestral locusAncestral proteinAncestral geneAncestral pathwayNew traitsBiochemical activityDifferent speciesGenesPmrB proteinEscherichia coliPhosphatase activityB resistanceProteinSalmonella enterica
2010
A Bacterial mRNA Leader that Employs Different Mechanisms to Sense Disparate Intracellular Signals
Park SY, Cromie MJ, Lee EJ, Groisman EA. A Bacterial mRNA Leader that Employs Different Mechanisms to Sense Disparate Intracellular Signals. Cell 2010, 142: 737-748. PMID: 20813261, PMCID: PMC2967377, DOI: 10.1016/j.cell.2010.07.046.Peer-Reviewed Original ResearchMeSH Keywords5' Untranslated RegionsAdenosine TriphosphatasesBacterial ProteinsBase SequenceGene Expression Regulation, BacterialMagnesiumMembrane Transport ProteinsMolecular Sequence DataProlineRegulatory Sequences, Ribonucleic AcidRNA, MessengerSalmonella typhimuriumSequence AlignmentTranscription, GeneticConceptsLeader sequenceDefining the Plasticity of Transcription Factor Binding Sites by Deconstructing DNA Consensus Sequences: The PhoP-Binding Sites among Gamma/Enterobacteria
Harari O, Park SY, Huang H, Groisman EA, Zwir I. Defining the Plasticity of Transcription Factor Binding Sites by Deconstructing DNA Consensus Sequences: The PhoP-Binding Sites among Gamma/Enterobacteria. PLOS Computational Biology 2010, 6: e1000862. PMID: 20661307, PMCID: PMC2908699, DOI: 10.1371/journal.pcbi.1000862.Peer-Reviewed Original ResearchMeSH KeywordsArtificial IntelligenceBacterial ProteinsBase SequenceBinding SitesChromatin ImmunoprecipitationCluster AnalysisComputational BiologyConsensus SequenceDNA, BacterialEnterobacteriaceaeEvolution, MolecularGene Expression ProfilingGenome, BacterialModels, GeneticMolecular Sequence DataNucleic Acid ConformationOligonucleotide Array Sequence AnalysisPattern Recognition, AutomatedSequence AlignmentTranscription FactorsConceptsGene expressionSite sequenceKey cis-regulatory elementsExpression of dozensGenome-wide analysisCis-regulatory elementsTranscription Factor Binding SitesDifferential gene expressionSpecific DNA sequencesDNA consensus sequencePhoP proteinAncestral geneTarget promotersDistant speciesHigh conservationTranscriptional regulatorsInter-species differencesChromatin immunoprecipitationRelated speciesRNA polymeraseDNA sequencesTarget genesRegulatory proteinsMolecular basisConsensus sequenceAn antisense RNA that governs the expression kinetics of a multifunctional virulence gene
Lee EJ, Groisman EA. An antisense RNA that governs the expression kinetics of a multifunctional virulence gene. Molecular Microbiology 2010, 76: 1020-1033. PMID: 20398218, PMCID: PMC2909850, DOI: 10.1111/j.1365-2958.2010.07161.x.Peer-Reviewed Original ResearchConceptsAntisense RNAGenome-wide transcriptome analysisRegulatory protein PhoPLong antisense RNAProtein levelsAntisense transcriptionMgtC proteinTranscriptome analysisRNase EAntisense transcriptsPolycistronic messageRNase IIISalmonella virulenceBacterial speciesPhysiological roleExpression kineticsTranscriptionRNAVirulence genesApparent roleVirulencePhoPSalmonella entericaMgtCAmgRS
2009
Short-Term Signatures of Evolutionary Change in the Salmonella enterica Serovar Typhimurium 14028 Genome
Jarvik T, Smillie C, Groisman EA, Ochman H. Short-Term Signatures of Evolutionary Change in the Salmonella enterica Serovar Typhimurium 14028 Genome. Journal Of Bacteriology 2009, 192: 560-567. PMID: 19897643, PMCID: PMC2805332, DOI: 10.1128/jb.01233-09.Peer-Reviewed Original ResearchMeSH KeywordsEvolution, MolecularGenome, BacterialModels, GeneticMolecular Sequence DataSalmonella typhimuriumConceptsComplete genomic sequenceGenomic sequencesSalmonella enterica serovar TyphimuriumTyphoid-like diseaseEnterica serovar TyphimuriumEvolutionary changeSequence evolutionGram-negative pathogensS. typhimuriumSerovar TyphimuriumComplete inventoryGenetic alterationsAvirulent strainsS. entericaPathogenic organismsSequenceLaboratory passageS. typhimurium strainTyphimuriumGenomeStrainsTyphimurium strainsLT2 strainOrganismsProgenitorsIdentifying promoter features of co-regulated genes with similar network motifs
Harari O, del Val C, Romero-Zaliz R, Shin D, Huang H, Groisman EA, Zwir I. Identifying promoter features of co-regulated genes with similar network motifs. BMC Bioinformatics 2009, 10: s1. PMID: 19426448, PMCID: PMC2681069, DOI: 10.1186/1471-2105-10-s4-s1.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceBinding SitesComputational BiologyDNA-Directed RNA PolymerasesEscherichia coliGene Expression Regulation, BacterialGene Regulatory NetworksGenome, BacterialMolecular Sequence DataPromoter Regions, GeneticRegulatory Sequences, Nucleic AcidSalmonella typhiTranscription FactorsConceptsTranscriptional regulatorsPromoter featuresNetwork motifsTranscription factorsTarget genesRegulatory proteinsPhoP/PhoQ regulatory systemExpression patternsGene expressionCo-regulated genesGroup of genesGene regulatory networksDifferential gene expressionCis-acting elementsDifferent expression patternsCharacteristic expression patternsSalmonella enterica serovar TyphimuriumProteobacterial genomesPhoP proteinEnterica serovar TyphimuriumRegulatory networksRNA polymeraseRegulatory regionsRepression siteMultiple promoters
2008
Evolution and Dynamics of Regulatory Architectures Controlling Polymyxin B Resistance in Enteric Bacteria
Mitrophanov AY, Jewett MW, Hadley TJ, Groisman EA. Evolution and Dynamics of Regulatory Architectures Controlling Polymyxin B Resistance in Enteric Bacteria. PLOS Genetics 2008, 4: e1000233. PMID: 18949034, PMCID: PMC2565834, DOI: 10.1371/journal.pgen.1000233.Peer-Reviewed Original ResearchConceptsRegulatory architectureComplex genetic networksDirect transcriptional controlEnteric bacteriaPolymyxin B resistanceEvolutionary historyTranscriptional controlGenetic networksRegulatory proteinsRegulatory pathwaysCellular responsesStructural modulesIndirect regulationRapid activationB resistanceExpression levelsMRNA expression levelsAntibiotic polymyxin BRegulation circuitBacteriaInducible resistanceFunctional propertiesProteinSystem postTransitional stageOvercoming H-NS-mediated Transcriptional Silencing of Horizontally Acquired Genes by the PhoP and SlyA Proteins in Salmonella enterica *
Perez JC, Latifi T, Groisman EA. Overcoming H-NS-mediated Transcriptional Silencing of Horizontally Acquired Genes by the PhoP and SlyA Proteins in Salmonella enterica *. Journal Of Biological Chemistry 2008, 283: 10773-10783. PMID: 18270203, PMCID: PMC2447644, DOI: 10.1074/jbc.m709843200.Peer-Reviewed Original ResearchConceptsHistone-like nucleoid structuring proteinPagC geneSlyA proteinRNA polymeraseRNA polymerase recruitmentH-NS repressionNucleoid structuring proteinHorizontal gene transferDifferent regulatory proteinsSalmonella entericaPolymerase recruitmentTranscriptional silencingNew traitsForeign DNAGene transcriptionRegulatory proteinsUgtLRespective promotersTranscriptionPhoPRecipient organismGenesPagC promoterGene transferProtein
2006
The PhoP/PhoQ two-component system stabilizes the alternative sigma factor RpoS in Salmonella enterica
Tu X, Latifi T, Bougdour A, Gottesman S, Groisman EA. The PhoP/PhoQ two-component system stabilizes the alternative sigma factor RpoS in Salmonella enterica. Proceedings Of The National Academy Of Sciences Of The United States Of America 2006, 103: 13503-13508. PMID: 16938894, PMCID: PMC1557385, DOI: 10.1073/pnas.0606026103.Peer-Reviewed Original ResearchConceptsSigma factor RpoSPhoP/PhoQTwo-component systemAlternative sigma factor RpoSTwo-component regulatory system PhoP/PhoQPhoP/PhoQ.Stress response genesSalmonella enterica serovar TyphimuriumRpoS stabilityClpXP proteaseTranscriptional activatorEnterica serovar TyphimuriumRegulatory circuitsRpoS mutantResponse genesRegulatory proteinsProtein turnoverRpoSBacterial speciesEscherichia coliPhoP geneGenesSerovar TyphimuriumE. coliPhoQIdentification of the lipopolysaccharide modifications controlled by the Salmonella PmrA/PmrB system mediating resistance to Fe(III) and Al(III)
Nishino K, Hsu FF, Turk J, Cromie MJ, Wösten MM, Groisman EA. Identification of the lipopolysaccharide modifications controlled by the Salmonella PmrA/PmrB system mediating resistance to Fe(III) and Al(III). Molecular Microbiology 2006, 61: 645-654. PMID: 16803591, PMCID: PMC1618816, DOI: 10.1111/j.1365-2958.2006.05273.x.Peer-Reviewed Original ResearchMeSH KeywordsAluminumBacterial ProteinsBase SequenceDrug Resistance, BacterialEscherichia coli ProteinsGene Expression Regulation, BacterialIronLipid ALipopolysaccharidesMolecular Sequence DataMutationPeriplasmPhosphoric Monoester HydrolasesPhosphorylationPolymyxin BSalmonella typhimuriumSoil MicrobiologyTranscription FactorsConceptsPmrA/PmrB systemGram-negative bacterial speciesNon-host environmentsPmrA/PmrBWild-type strainSalmonella enterica serovar TyphimuriumEnterica serovar TyphimuriumOuter membraneLipopolysaccharide modificationBacterial speciesCovalent modificationResistance genesSerovar TyphimuriumOxygen-dependent killingPmrAEssential metalsHomeostatic mechanismsSalmonella survivalMutantsDephosphorylationGenesSpeciesProteinMajor constituentsIdentificationThe PmrA/PmrB and RcsC/YojN/RcsB systems control expression of the Salmonella O‐antigen chain length determinant
Delgado MA, Mouslim C, Groisman EA. The PmrA/PmrB and RcsC/YojN/RcsB systems control expression of the Salmonella O‐antigen chain length determinant. Molecular Microbiology 2006, 60: 39-50. PMID: 16556219, DOI: 10.1111/j.1365-2958.2006.05069.x.Peer-Reviewed Original ResearchConceptsPmrA/PmrBO-antigen subunitSame start siteHydrophobic lipid ASDS/PAGE gelsChain length determinantTwo-component systemSalmonella enterica serovar TyphimuriumO-antigenGram-negative bacteriaNull mutantsEnterica serovar TyphimuriumStart siteRcsB mutantDifferent environmental conditionsCell envelopeRegulatory proteinsLPS genesOutermost componentCore oligosaccharideSerovar TyphimuriumGenesEnvironmental conditionsPAGE gelsRcsBA Mg2+-responding RNA That Controls the Expression of a Mg2+ Transporter
GROISMAN EA, CROMIE MJ, SHI Y, LATIFI T. A Mg2+-responding RNA That Controls the Expression of a Mg2+ Transporter. Cold Spring Harbor Symposia On Quantitative Biology 2006, 71: 251-258. PMID: 17381304, DOI: 10.1101/sqb.2006.71.005.Peer-Reviewed Original ResearchConceptsDifferent cellular compartmentsAbundant divalent cationPhoP/PhoQStem-loop structureDifferent stem-loop structuresSensor PhoQTransporter MgtAMgtA geneMgtA transcriptionCellular compartmentsGene transcriptionTranscriptionPhoPPhoQMgtATransportersDisparate stepsBiological systemsDivalent cationsAdditional Mg2Singular exampleExpressionEnzymatic reactionsRiboswitchCytoplasmic Mg2